Hi @yzhang2168 – the data in the entropy panel is generated within auspice (the visualisation app which is displaying the tree, entropy panel etc) from the mutations which have been inferred across the tree by augur. The augur commands which generate these are
augur ancestral (infers nucleotide mutations up the tree) and
augur translate (nt -> aa). This section of the docs explains a bit more on what entropy & events mean, as well as showing how to download these data in TSV format from auspice. Note also that we mask certain sites in the genome for our SARS-CoV-2 analysis – details in the repo.
Are the mutations shown [on a branch/tip] only include those that are new when compared with the immediate parent?
Yes, that’s correct. If you change the tree view to “divergence” (via the controls in the sidebar) then you can see a count of nucleotide changes relative to the (inferred) root sequence.
P.S. If there’s a technical reason you haven’t been able to run nextstrain on your computer please let us know and we’ll try to help!